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core-metrics-phylogenetic: Core diversity metrics (phylogenetic and non-phylogenetic)ΒΆ

Docstring:

Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]

  Applies a collection of diversity metrics (both phylogenetic and non-
  phylogenetic) to a feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table containing the samples over which
                          diversity metrics should be computed.     [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     correspond to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [required]
Parameters:
  --p-sampling-depth INTEGER
    Range(1, None)        The total frequency that each sample should be
                          rarefied to prior to computing diversity metrics.
                                                                    [required]
  --m-metadata-file METADATA...
    (multiple arguments   The sample metadata to use in the emperor plots.
     will be merged)                                                [required]
  --p-with-replacement / --p-no-with-replacement
                          Rarefy with replacement by sampling from the
                          multinomial distribution instead of rarefying
                          without replacement.                [default: False]
  --p-n-jobs-or-threads NTHREADS
                          [beta/beta-phylogenetic methods only] - The number
                          of concurrent jobs or CPU threads to use in
                          performing this calculation. Individual methods will
                          create jobs/threads as implemented in
                          q2-diversity-lib dependencies. May not exceed the
                          number of available physical cores. If
                          n-jobs-or-threads = 'auto', one thread/job will be
                          created for each identified CPU core on the host.
                                                                  [default: 1]
  --p-ignore-missing-samples / --p-no-ignore-missing-samples
                          If set to `True` samples and features without
                          metadata are included by setting all metadata values
                          to: "This element has no metadata". By default an
                          exception will be raised if missing elements are
                          encountered. Note, this flag only takes effect if
                          there is at least one overlapping element.
                                                              [default: False]
Outputs:
  --o-rarefied-table ARTIFACT FeatureTable[Frequency]
                          The resulting rarefied feature table.     [required]
  --o-faith-pd-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Faith PD values by sample.      [required]
  --o-observed-features-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Observed Features values by sample.
                                                                    [required]
  --o-shannon-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Shannon diversity values by sample.
                                                                    [required]
  --o-evenness-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Pielou's evenness values by sample.
                                                                    [required]
  --o-unweighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of unweighted UniFrac distances between
                          pairs of samples.                         [required]
  --o-weighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of weighted UniFrac distances between pairs
                          of samples.                               [required]
  --o-jaccard-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Jaccard distances between pairs of
                          samples.                                  [required]
  --o-bray-curtis-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Bray-Curtis distances between pairs of
                          samples.                                  [required]
  --o-unweighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from unweighted UniFrac
                          distances between samples.                [required]
  --o-weighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from weighted UniFrac
                          distances between samples.                [required]
  --o-jaccard-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Jaccard distances between
                          samples.                                  [required]
  --o-bray-curtis-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Bray-Curtis distances
                          between samples.                          [required]
  --o-unweighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          unweighted UniFrac.                       [required]
  --o-weighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          weighted UniFrac.                         [required]
  --o-jaccard-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Jaccard.                                  [required]
  --o-bray-curtis-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Bray-Curtis.                              [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this pipeline. If not provided, the default
                          cache under $TMP/qiime2/ will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.diversity.pipelines import core_metrics_phylogenetic

Docstring:

Core diversity metrics (phylogenetic and non-phylogenetic)

Applies a collection of diversity metrics (both phylogenetic and non-
phylogenetic) to a feature table.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples over which diversity metrics
    should be computed.
phylogeny : Phylogeny[Rooted]
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
sampling_depth : Int % Range(1, None)
    The total frequency that each sample should be rarefied to prior to
    computing diversity metrics.
metadata : Metadata
    The sample metadata to use in the emperor plots.
with_replacement : Bool, optional
    Rarefy with replacement by sampling from the multinomial distribution
    instead of rarefying without replacement.
n_jobs_or_threads : Threads, optional
    [beta/beta-phylogenetic methods only] - The number of concurrent jobs
    or CPU threads to use in performing this calculation. Individual
    methods will create jobs/threads as implemented in q2-diversity-lib
    dependencies. May not exceed the number of available physical cores. If
    n_jobs_or_threads = 'auto', one thread/job will be created for each
    identified CPU core on the host.
ignore_missing_samples : Bool, optional
    If set to `True` samples and features without metadata are included by
    setting all metadata values to: "This element has no metadata". By
    default an exception will be raised if missing elements are
    encountered. Note, this flag only takes effect if there is at least one
    overlapping element.

Returns
-------
rarefied_table : FeatureTable[Frequency]
    The resulting rarefied feature table.
faith_pd_vector : SampleData[AlphaDiversity]
    Vector of Faith PD values by sample.
observed_features_vector : SampleData[AlphaDiversity]
    Vector of Observed Features values by sample.
shannon_vector : SampleData[AlphaDiversity]
    Vector of Shannon diversity values by sample.
evenness_vector : SampleData[AlphaDiversity]
    Vector of Pielou's evenness values by sample.
unweighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of unweighted UniFrac distances between pairs of samples.
weighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of weighted UniFrac distances between pairs of samples.
jaccard_distance_matrix : DistanceMatrix
    Matrix of Jaccard distances between pairs of samples.
bray_curtis_distance_matrix : DistanceMatrix
    Matrix of Bray-Curtis distances between pairs of samples.
unweighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from unweighted UniFrac distances between samples.
weighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from weighted UniFrac distances between samples.
jaccard_pcoa_results : PCoAResults
    PCoA matrix computed from Jaccard distances between samples.
bray_curtis_pcoa_results : PCoAResults
    PCoA matrix computed from Bray-Curtis distances between samples.
unweighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from unweighted UniFrac.
weighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from weighted UniFrac.
jaccard_emperor : Visualization
    Emperor plot of the PCoA matrix computed from Jaccard.
bray_curtis_emperor : Visualization
    Emperor plot of the PCoA matrix computed from Bray-Curtis.